The problem here is an equal number of people want to be indestructible, as there are people wanting to be challenged at all times. The solution I was going for was to be able to choose how you end up. To increase your health you have to give up half your skill points for that level, endurance still affects the base hlth ad how much it increases by but you determine when it increases.
This doesn't even need to be from the start, it could add health anyway for the first ten levels (your still not too powerful level usually) and then require you telling it too, this system ensures you can never master everything and take on death claws naked.
All the enemies need to improved to some degree, but you or them being bullet sponges stinks of bad game design.
I don't want to be indestructible. Far from it. However, while a radroach should be a pain at level one, I should be stomping on it by level ten. They should not be difficult for the entire game. Likewise there needs to be enemies I have to grow into. And even when I've reached max level, max HP, with the best armor and the best weapons, there needs to be enemies I still fear. I agree that bullet sponges don't do it. They need to be able to dish out as well as they receive. I shouldn't be able to just waltz in, guns blazing without a worry. And you don't have to gimp the PC to achieve that.
My idea was to have endurance have a greater influence on HP gain at level-up. That way, a character with an endurance of, say, three might have a similar starting HP as a character with an endurance of eight. But by as you level up, the discrepancy between the two begins to widen, so that by max level it's a significant and noticeable difference. If you want a character that can take a beating, then you put more of your SPECIAL points into endurance. If you choose to put those points somewhere else, you'll feel the difference in the long run.